{"title":"An investigation into the usage of black cumin derivatives against cancer and COVID-19 as the nature medicine.","authors":"Faik Gökalp","doi":"10.1080/07391102.2024.2302942","DOIUrl":"10.1080/07391102.2024.2302942","url":null,"abstract":"<p><p>Black cumin has been used as a spice and food preservative for years. Thymol, thymoquinone, thymohydroquinone and dihydrothymoquinone are the most important natural agents in black cumin. In order to determine the most active compound in black cumin the theoretical calculations have been carried out in different phases by using the density functional theory (DFT). The inhibition effect of black cumin derivatives on Histone deacetylase 2 (HDAC2) has been determined and supported the experimental studies without losing time and matter. The chemical activity, stability and solubility of the active substances in black cumin have been theoretically calculated. The chemical active compounds had been investigated in the black seeds when extracted with water. Their stability and polarity in blood and water are important parameters. HDAC2- dihydrothymoquinone interaction has been investigated. It has been determined that the active substances found in black cumin are very effective in protecting ACE2 against COVID-19 and by comparing the docking results of important receptors and selected ligands on COVID-19.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4362-4369"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"NetVA: an R package for network vulnerability and influence analysis.","authors":"Swapnil Kumar, Grace Pauline, Vaibhav Vindal","doi":"10.1080/07391102.2024.2303607","DOIUrl":"10.1080/07391102.2024.2303607","url":null,"abstract":"<p><p>In biological network analysis, identifying key molecules plays a decisive role in the development of potential diagnostic and therapeutic candidates. Among various approaches of network analysis, network vulnerability analysis is quite important, as it assesses significant associations between topological properties and the functional essentiality of a network. Similarly, some node centralities are also used to screen out key molecules. Among these node centralities, escape velocity centrality (EVC), and its extended version (EVC+) outperform others, <i>viz.</i>, Degree, Betweenness, and Clustering coefficient. Keeping this in mind, we aimed to develop a first-of-its-kind R package named NetVA, which analyzes networks to identify key molecular players (individual proteins and protein pairs/triplets) through network vulnerability and EVC+-based approaches. To demonstrate the application and relevance of our package in network analysis, previously published and publicly available protein-protein interactions (PPIs) data of human breast cancer were analyzed. This resulted in identifying some most important proteins. These included essential proteins, non-essential proteins, hubs, and bottlenecks, which play vital roles in breast cancer development. Thus, the NetVA package, available at https://github.com/kr-swapnil/NetVA with a detailed tutorial to download and use, assists in predicting potential candidates for therapeutic and diagnostic purposes by exploring various topological features of a disease-specific PPIs network.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4552-4563"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139485603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Simulation and practical investigation of carbonic anhydrase stability in an industrial solvent system of methyl diethanolamine for carbon dioxide capture.","authors":"Ebrahim Barzegari, Shima Ghaedizadeh, Aminollah Pourshohod, Majid Zeinali, Mostafa Jamalan","doi":"10.1080/07391102.2024.2305311","DOIUrl":"10.1080/07391102.2024.2305311","url":null,"abstract":"<p><p>Carbonic anhydrase owing to its potential as an industrial biocatalyst for carbon dioxide sequestration from flue gas has attracted considerable attention in solving global warming problems. A large body of research has been conducted to increase the thermal stability of carbonic anhydrase from different sources against the harsh operational conditions of CO<sub>2</sub> capture systems. In contrast to cost-intensive protein engineering methods, solvation with aqueous-organic binary mixtures offers a convenient and economical alternative strategy for retention of protein structure and stability. This study aimed to examine the stabilizing effect of methyl diethanolamine (MDEA) as a component of an aqueous-organic solvent mixture on human carbonic anhydrase II (HCA II) at extreme temperatures. Computational and also spectroscopic examinations were employed for tracking conformational changes and stability evaluation of HCA II in 50:50 (vol %) water: MDEA binary mixture at high temperature. Molecular dynamic (MD) simulation studies predicted the high thermal stability of HCA II in the presence of MDEA. UV absorbance spectra confirmed the thermo-stabilizing effect of the binary solvent mixture on HCA II. While the enzymatic activity of HCA II at 25 °C in the presence of 10, 25, and 50 (vol%) of MDEA was substantially increased, no obvious effect on retention of HCA II activity in the water-MDEA binary solvent mixture at 85 °C was seen. It is shown that the solvation of HCA II in the presence of MDEA could result in the prevention of aggregate formation in high temperatures but not functional stability.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4743-4752"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139485639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sanghati Roy Chowdhury, Redam Saha, Tirthankar Koley, Farah Naz, Saurabh Sharma, Mohd Imran Khan, Manoj Kumar, Punit Kaur, Abdul S Ethayathulla
{"title":"Structure-based identification of potential natural compound inhibitors targeting bacterial cytoskeleton protein FtsZ from <i>Acinetobacter baumannii</i> by computational studies.","authors":"Sanghati Roy Chowdhury, Redam Saha, Tirthankar Koley, Farah Naz, Saurabh Sharma, Mohd Imran Khan, Manoj Kumar, Punit Kaur, Abdul S Ethayathulla","doi":"10.1080/07391102.2024.2304675","DOIUrl":"10.1080/07391102.2024.2304675","url":null,"abstract":"<p><p><i>Acinetobacter baumannii</i> is one of the multi-drug-resistant pathogens responsible for hospital-acquired infections reported worldwide. Clinically it is challenging to treat these pathogens as they have developed resistance against the existing class of antibiotics. Hence, there is an urgent need to develop a new class of antibiotics against these pathogens to prevent the spread of infections and mortality. In <i>Acinetobacter baumannii</i>, the filamentous temperature-sensitive mutant Z protein polymerizes at the imminent division site to form a Z-ring at the mid-point of the cell and act as a scaffold to recruit other cell division proteins involved in orchestrating septum synthesis in bacteria. Perturbation in the assembly of FtsZ affects bacterial cell dynamics and survival. Hence, FtsZ has emerged as a new drug target in antibiotic discovery to identify compounds that inhibit bacterial cell division. In this study, we have performed a virtual screening of 30,000 compounds from the ZINC Biogenic natural compound library targeting the nucleotide-binding site of FtsZ from <i>Acinetobacter baumannii.</i> We have identified 8 new natural compounds with binding energy in the range of -8.66 to -6.953 kcal/mol and analyzed them by 200 ns molecular dynamics simulations. Out of these eight compounds, ZINC14708526 showed the best binding with relatively optimal drug-likeness and medicinal chemistry as a potent inhibitor of abFtsZ. Thus, the identified FtsZ inhibitor ZINC14708526 is a promising lead compound to develop potent antimicrobial agents against <i>Acinetobacter baumannii</i> infections.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4578-4590"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139491506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Priyani R Paligaspe, Samantha Weerasinghe, Dhammike P Dissanayake, Rajendram Senthilnithy, Thelma Abeysinghe, Chanika D Jayasinghe
{"title":"Computational investigation of impact of Pb(II) and Ni(II) ions on hUNG enzyme: insights from molecular dynamics simulations.","authors":"Priyani R Paligaspe, Samantha Weerasinghe, Dhammike P Dissanayake, Rajendram Senthilnithy, Thelma Abeysinghe, Chanika D Jayasinghe","doi":"10.1080/07391102.2024.2307442","DOIUrl":"10.1080/07391102.2024.2307442","url":null,"abstract":"<p><p>Human uracil DNA glycosylase (hUNG), a crucial player in the initiation of the base excision repair pathway, is susceptible to alterations in function and conformation induced by the accumulation of toxic metals. Despite the recognized impact of toxic metals on DNA repair enzymes, there exists a notable deficiency in theoretical investigations addressing this phenomenon. This study investigates the impact of toxic heavy metal ions, Pb(II) and Ni(II), on the stability of hUNG through molecular dynamics (MD) simulations. The initial analysis involved the identification of key cavities in the hUNG enzyme. Notably, the active site cavity emerged as a promising site for ligand binding. Subsequently, AutoDockTools software was employed to dock Pb(II) and Ni(II) onto the identified cavities, followed by extensive MD simulations. The MD analysis, encompassing parameters such as root mean square deviation, radius of gyration, solvent accessible surface area, hydrogen bond variations, Ramachandran plot, principal component analysis, and root mean square fluctuations, collectively revealed distinct alterations in the behavior of the enzyme upon complexation with Pb(II) and Ni(II). Interestingly, the enzyme exhibited enhanced structural stability, reduced flexibility, and modified hydrogen bonding patterns in the presence of these toxic metal ions. The observed limitation in structural flexibility implies a more rigid and stable conformation when the enzyme complex with Pb(II) and Ni(II) compared to its free form. This structural alteration may lead to a potential reduction in enzymatic activity, suggesting that toxic metal ions influence the functional dynamics of hUNG. These computational findings offer valuable insights into the molecular interactions between metal ions and enzymes.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4804-4813"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"HrpY protein of <i>Ralstonia solanacearum</i> exhibits spontaneous formation of pilus like assembly: analysis of its stability.","authors":"Naveen Arasakumar, Vikraam Loganathan, Ramanathan Natesh, Karthe Ponnuraj","doi":"10.1080/07391102.2024.2304678","DOIUrl":"10.1080/07391102.2024.2304678","url":null,"abstract":"<p><p>Type 3 secretory system (T3SS), a complex protein machinery has a unique virulence mechanism that involves injecting effector proteins directly into host cells. The T3SS effector proteins are transported through an extracellular long hollow needle made up of multiple copies of a small protein. In T3SS of the plant pathogen <i>Ralstonia solanacearum</i>, the 8.6 kDa HrpY protein assembles into a large needle like apparatus (pilus) for transporting effector proteins. To study structural details of HrpY, we recombinantly expressed and purified HrpY in <i>E. coli</i>. The dynamic light scattering (DLS) analysis showed that rHrpY has spontaneously formed oligomers of large order (>100 nm). Transmission electron microscopy of rHrpY samples revealed that the large structures are tube like assembly having dimensions 86.3-166.6 nm and 5.8-6.8 nm in length and width respectively. Different molecular sizes of the purified rHrpY hindered the crystallization of the protein. The stability of oligomer assembly was studied with denaturants and surfactants. Denaturants like urea and guanidine HCl could not break them apart; however, detergents like SDS, sarkosyl, Octyl<i>-</i>β<i>-</i>Glucoside, CHAPS, Tween 20, Tween 80 and Triton X-100 showed disassembly of the oligomer. rHrpY assembly was found to withstand up to 50 °C and the circular dichroism analysis revealed that there is no significant change in the secondary structural composition with increase in temperature. However, change in the secondary structure was observed with the addition of SDS.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4591-4602"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139478605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unveiling the potential of recently FDA-approved drugs as quorum sensing inhibitors against <i>P. Aeruginosa</i> using high-performance computational techniques.","authors":"Debanjan Dey, Anoop Kumar","doi":"10.1080/07391102.2024.2304682","DOIUrl":"10.1080/07391102.2024.2304682","url":null,"abstract":"<p><p>Through cell-to-cell communication, activation of efflux pumps, formation of biofilms, and other mechanisms, <i>pseudomonas aeruginosa's</i> quorum sensing systems (QSS), notably the lasl/las-r system, contribute a vital role in the development of anti-microbial resistance (AMR). Identifying potential drugs against these targets could have significant implications for combating <i>pseudomonal</i> infections. The current study aims to identify promising recently FDA-approved drugs against lasl/las-r proteins. The ligands were selected from the FDA-approved drug lists of the last 5 years. Out of 202, 78 drugs were checked for interaction with lasl/las-r protein and 4 drugs revealed top binding conformations characterized by favorable energetic profiles within the active site of the las-r protein which were further assigned for 250-ns molecular dynamics (MD) simulation. The MD analysis confirmed the dynamical stability of brexanolone and oteseconazole with las-r protein. The root mean square deviation (RMSD), radius of gyration (Rg) and solvent-accessible surface area (SASA) analysis have indicated less deviation, more compactness of protein and less exposure of protein ligand complex to its surroundings as compared to the reference ligand-protein complex. The hydroxyl group in the oteseconazole whereas hydroxyl and ketone group in the brexanolone were responsible for hydrogen bonds with the active site residue of las r ptotein as indicated by ligand-protein contacts diagram. The binding energies per residue analysis revealed TYR-47 as the most contributing amino acid residue for interaction with oteseconazole and brexanolone. The identified drugs may be potential repurposing candidates against <i>pseudomonal</i> infections through inhibition of las-r protein.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4698-4715"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139478614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification of amentoflavone as a potent SARS-CoV-2 M<sup>pro</sup> inhibitor: a combination of computational studies and in vitro biological evaluation.","authors":"Prabuddha Bhattacharya, Anirban Mandal","doi":"10.1080/07391102.2024.2304676","DOIUrl":"10.1080/07391102.2024.2304676","url":null,"abstract":"<p><p>Small-molecule inhibitors of SARS-CoV-2 M<sup>pro</sup> that block the active site pocket of the viral main protease have been considered potential therapeutics for the development of drugs against SARS-CoV-2. Here, we report the identification of amentoflavone (a biflavonoid) through docking-based virtual screening of a library comprised of 231 compounds consisting of flavonoids and isoflavonoids. The docking results were further substantiated through extensive analysis of the data obtained from all-atom 150 ns MD simulation. End-state effective free energy calculations using MM-PBSA calculations further suggested that (<i>R<sub>a</sub></i>)-amentoflavone (C3'-C8''-atropisomer) may show a greater binding affinity towards the M<sup>pro</sup> than (<i>S<sub>a</sub></i>)-amentoflavone. <i>In vitro</i> cytotoxicity assay established that amentoflavone showed a high CC<sub>50</sub> value indicating much lower toxicity. Further, potent inhibition of the M<sup>pro</sup> by amentoflavone was established by studying the effect on HEK293T cells treated with SARS-CoV-2 M<sup>pro</sup> expressing plasmid.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4659-4677"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139540816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Santosh K Rath, Rakesh K Nagar, Sanjib Das, Govind Yadav, Debaraj Mukherjee, Buddh Singh, Samar Singh, Payare L Sangwan
{"title":"C-30 analogues of betulinic acid as potent cytotoxic agents: design, synthesis, biological evaluation and <i>in-silico</i> studies.","authors":"Santosh K Rath, Rakesh K Nagar, Sanjib Das, Govind Yadav, Debaraj Mukherjee, Buddh Singh, Samar Singh, Payare L Sangwan","doi":"10.1080/07391102.2024.2303612","DOIUrl":"10.1080/07391102.2024.2303612","url":null,"abstract":"<p><p>In an endeavour to improve the anti-cancer activity of betulinic acid (BA), a series of C-30 derivatives were envisaged and synthesized with a novel synthetic approach. All the derivatives were evaluated for cytotoxic activity by MTT assay against six different human cancer cell lines: prostate (PC3), lung (A549), human hepatocellular carcinoma (HepG2), human leukemia (Molt-4), pancreatic (Panc-1) and breast (MCF-7). The data revealed that compound <b>16</b> was observed most promising cytotoxic agent with IC<sub>50</sub> values of <b>7.43 </b>μM, <b>9.1 </b>μM, and <b>9.64 </b>μM against A549, MCF-7, and PC3 cancer cell lines respectively. A further mechanistic study confirmed compound 16 showed significant cell death by arresting the cell cycle in the G1 phase and inducing apoptosis in A549 cells.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4564-4577"},"PeriodicalIF":2.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139996359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Targeting <i>Mycobacterium tuberculosis</i>: identification of potential phytochemicals from traditional plants against glucosyl-3-phosphoglycerate phosphatase (GpgP).","authors":"Pratyaksha Singh, Saurabh Kumar Bhati, Monika Jain, Rashmi Prabha Singh, Jayaraman Muthukumaran, Amit Kumar Singh","doi":"10.1080/07391102.2025.2509789","DOIUrl":"https://doi.org/10.1080/07391102.2025.2509789","url":null,"abstract":"<p><p>Tuberculosis (TB) is a transmissible disease that causes severe infections in adults as well as in infants, as they have immature immune systems. Lungs are the main site for pulmonary TB infection, although TB can affect other parts like lymph nodes, bone, joints, etc., which is known as extrapulmonary TB. <i>M. tuberculosis</i> is becoming one of the world's most severe pathogens due to growing multidrug resistance (MDR) and extensively drug resistance (XDR), rendering treatment medications useless. GpgP was chosen as the promising drug target protein in this study because it is primarily involved in the catalysis of the second step in the production of Methylglucose lipopolysaccharides (MGLPs), which regulate the synthesis of mycolic acids, which are an essential component for building the mycobacterial cell envelope. The cell envelope of <i>M. tuberculosis</i> is unique and is responsible for the bacteria's flexibility and pathogenicity. An <i>in-house</i> library of phytochemicals was utilized for screening in AutoDock Vina, and then the ligands were docked using AutoDock with the drug target protein for further validation. Then, four ligands were filtered out using SwissADME that were further studied by performing molecular dynamic simulations. After a thorough analysis, CID_446611 and CID_5282146 ligands were identified as potential inhibitors of GpgP.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-9"},"PeriodicalIF":2.7,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}